I don't know what word to use to decribe when the Doctor punishes someone when they do something he doesn't like.

That's one of the reasons why he keeps running. The Master is always mocking him for doing this. If he didn't run, then he would probably have to result to violence.

Which he did after the Family of Blood wouldn't leave him alone. Ten never gave second chances. He had quite the reputation of being dangerous. Eleven was always reminded of that

I'll admit someone usually pushes it too far. His enemies think his ability to be sympathetic is a weakness but its what can motivate him to lose rational thought if someone he cares about gets hurt.